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Obtaining river or sea pebbles from local resources for concrete production is considered an economical and eco-friendly alternative, particularly in marine and island-offshore engineering. However, the resulting changes in the mechanical properties of these concrete have attracted attention. This study investigates the compressive behavior of concretes where river or sea pebbles partially (i.e., 33% and 67%) or fully (i.e., 100%) replace traditional gravel as coarse aggregate, using a noncontact full-field deformation measurement system based on digital image correlation (DIC). Compared to the traditional gravel concrete (GC), compressive strengths of the river pebble concrete (RPC) at constitution rates of 33%, 67%, and 100% decreased by 6.5%, 29.8%, and 38.9% while those values of the sea pebble concrete (SPC) decreased by 13.1%, 32.7%, and 44.3%, respectively. Meanwhile, SPC exhibited slightly lower compressive strength than RPC. The peak strains of both SPC and RPC decreased at lower substitution rates, although their stress-strain curves resembled those of GC. In contrast, RPC and SPC at higher substitution rates exhibited a noticeable stage of load hardening. Full-field deformation data and interfacial characteristics indicated that the compressive failure modes of both RPC and SPC showed significant interfacial slipping between pebbles and mortar with increasing coarse aggregate substitution rates. In comparison, fractures in coarse aggregate and mortar were observed in damaged GC. The study demonstrated that the spatio-temporal compressive deformation response and failure modes of SPC and RPC were distinct due to the introduction of pebbles, providing insights for engineering applications of river/sea pebble concrete in practical offshore or island construction projects. [ABSTRACT FROM AUTHOR]

Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. Caragana species are ecologically valuable for their roles in windbreaking and sand fixation. However, the taxonomy and phylogenetic relationships of the genus Caragana are still unclear. In this study, we sequenced and assembled the chloroplast genomes of representative species of Caragana and reconstructed robust phylogenetic relationships at the section level. The Caragana chloroplast genome has lost the inverted repeat region and wascategorized in the inverted repeat loss clade (IRLC). The chloroplast genomes of the eight species ranged from 128,458 bp to 135,401 bp and contained 110 unique genes. All the Caragana chloroplast genomes have a highly conserved structure and gene order. The number of long repeats and simple sequence repeats (SSRs) showed significant variation among the eight species, indicating heterogeneous evolution in Caragana. Selective pressure analysis of the genes revealed that most of the protein-coding genes evolved under purifying selection. The phylogenetic analyses indicated that each section forms a clade, except the section Spinosae, which was divided into two clades. This study elucidated the evolution of the chloroplast genome within the widely distributed genus Caragana. The detailed information obtained from this study can serve as a valuable resource for understanding the molecular dynamics and phylogenetic relationships within Caragana. [ABSTRACT FROM AUTHOR]

The use of oilseed rape (OS, Brassica napus L.) as a winter green manure is crucial for enhancing soil fertility and reducing chemical N application in paddy fields. However, the impacts of replacing varying amounts of chemical N with OS on CH4 and N2O emissions in paddy soils have not been well evaluated. In this study, GHG emissions, soil properties and OS decomposition in a rice-ratooning system with different OS-urea N replacement rates (0%, 25%, 50%, 75% and 100%) were investigated. Our results indicate that 84.7–90.7% of the initial C and 97.5–98.4% of the N were released during the 192-day decomposition process, and that the mineralization patterns of net C and net N in the OS residue were consistent with a single exponential decay model. The lowest CH4 emissions (9.97 g m−2) were observed at 0% OS, while the highest N2O emissions (0.40 g m−2) were observed at this level of substitution. Conversely, the highest CH4 emissions (20.71 g m−2) and lowest N2O emissions (0.07 g m−2) were observed at 100% OS. Compared to 0% substitution, 25% substitution significantly decreased GWP and GHGI without reducing rice grain yield. Environmental parameters such as soil redox, NH4+-N and residual N and C were shown to be significantly associated with CH4 emissions, whereas soil redox, NH4+-N and residual C were the main drivers of N2O emissions. In conclusion, 25% substitution of OS was the most cost-effective measure for balancing greenhouse gas emission and rice yield. [ABSTRACT FROM AUTHOR]

In this study, Afşin Elbistan C-type fly ash (FA) was used, which protects against the sulphate reaction that damages concrete. The detrimental effects of post-reaction decrease with increasing fly ash fineness. The study used 10%, 30%, and 50% weight substitutes of cement. The fly ash was ground in a ball mill for 0, 10, 20, 30, 45, and 60 min, and Blaine fineness values of 1555, 1632, 2347, 2589, 2766, and 3433 cm2/g were obtained, respectively. The effect of the samples on the sulphate resistance was investigated by exposing the samples to 5% or 10% added sulphate solutions, and the compressive strength and ultrasonic pulse velocity of the concrete were tested. The compressive strength values obtained decreased with the increase in sulphate content, and the increase in the grinding time and the amount of substituted FA increased the compressive strength values. It was observed that weight loss increased with increasing sulphate content and decreased with the addition of FA with a high Blaine fineness. It was determined that as the Blaine fineness value increased, the sulphate content, FA substitution amount, and ultrasonic pulse speed decreased. This study was carried out to determine the effects of fly ash used at different fineness and replacement ratios on the performance and strength of concrete after exposure to external influences such as sulphate. The use of fly ash instead of cement will reduce the use of waste materials and natural resources and prevent environmental pollution. The cost of cement and concrete will be reduced. [ABSTRACT FROM AUTHOR]

Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of H. perforatum and compared the genome variation among five Hypericum species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the Hypericum chloroplast genomes. The H. perforatum chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The H. perforatum chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. Hypericum chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five Hypericum species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes—trnK-UUU, infA, and rps16—were lost, and three genes—rps7, rpl23, and rpl32—were pseudogenized in Hypericum. All the Hypericum chloroplast genomes lost the two introns in clpP, the intron in rps12, and the second intron in ycf3. Hypericum chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection. [ABSTRACT FROM AUTHOR]

Previous studies on winter supplementation of growing cattle grazing stockpiled native Campos grasslands suggest that forage allowance (FA), herbage mass, and weather conditions before and during the supplementation period could all affect supplement feed efficiency (SFE)—that is, the difference or change in average daily gain (ADG) between supplemented (S) and control (C) animals (ADGchng, kg) per unit (kg) of supplement dry matter (DM) intake. In this study, we analyse data from fifteen collated winter supplementation trials carried out in Uruguay between 2004 and 2018. The working hypotheses of this research paper were: (i) that average substitution rates are positive, and (ii) that ADGchng is not constant throughout the supplementation period and that its variation may be attributed to sward, animal or weather variables. There were two main objectives: (i) to estimate the average supplement substitution rate (sSbR, kg forage, f, dry matter, DM intake reduction: kg supplement DM intake) and potential herbage intake substitution rate (hSbR, kg fDM intake reduction: kg fDM intake of control animals), and its association with SFE, and, (ii) to assess the existence of different phases and supplementation response patterns and its association with other relevant variables. Estimated substitution rates were always positive (sSbR = 0.3–1.1 kg/kg; hSbR = 0.1–0.3 kg/kg) and were negatively and moderately associated with SFE. Supplementation proved to be a dynamic process where three possible supplementation responses over the supplementation period were identified (linear, quadratic and Weibull). While linear patterns did not appear distinctly associated with any particular set of variables, quadratic models were mostly associated with herbage biomass and substitution rates, whereas Weibull models were the clearest in their association with frosts. Regardless of the response pattern, at the beginning of the trials it was the animals' body weight and supplement quality that most influenced supplement response, whereas towards the end, supplementation intake, supplemented animals' ADG and forage quality played a more relevant role. The estimated parameters and response patterns are expected to be used as inputs in decision support systems for livestock farmers in the future. [ABSTRACT FROM AUTHOR]

Until 2020, there were only three original complete genome (CG) nucleotide sequences of Omsk hemorrhagic fever virus (OHFV) in GenBank. For this reason, the evolutionary rate and divergence time assessments reported in the literature were based on the E gene sequences, but notably without temporal signal evaluation, such that their reliability is unclear. As of July 2022, 47 OHFV CG sequences have been published, which enables testing of temporal signal in the data and inferring unbiased and reliable substitution rate and divergence time values. Regression analysis in the TempEst software demonstrated a stronger clocklike behavior in OHFV samples for the complete open reading frame (ORF) data set (R2 = 0.42) than for the E gene data set (R2 = 0.11). Bayesian evaluation of temporal signal indicated very strong evidence, with a log Bayes factor of more than 5, in favor of temporal signal in all data sets. Our results based on the complete ORF sequences showed a more precise OHFV substitution rate (95% highest posterior density (HPD) interval, 9.1 × 10−5–1.8 × 10−4 substitutions per site per year) and tree root height (416–896 years ago) compared with previous assessments. The rate obtained is significantly higher than tick-borne encephalitis virus by at least 3.8-fold. The phylogenetic analysis and past population dynamics reconstruction revealed the declining trend of OHFV genetic diversity, but there was phylogenomic evidence that implicit virus subpopulations evolved locally and underwent an exponential growth phase. [ABSTRACT FROM AUTHOR]

We evaluated the temporal signal and substitution rate of tick-borne encephalitis virus (TBEV) using 276 complete open reading frame (ORF) sequences with known collection dates. According to a permutation test, the TBEV Siberian subtype (TBEV-S) data set has no temporal structure and cannot be applied for substitution rate estimation without other TBEV subtypes. The substitution rate obtained suggests that the common clade of TBEV (TBEV-common), including all TBEV subtypes and louping-ill virus (LIV), is characterized by the lowest rate (1.87 × 10−5 substitutions per site per year (s/s/y) or 1 nucleotide substitution per ORF per 4.9 years; 95% highest posterior density (HPD) interval, 1.3–2.4 × 10−5 s/s/y) among all tick-borne flaviviruses previously assessed. Within TBEV-common, the TBEV European subtype (TBEV-E) has the lowest substitution rate (1.3 × 10−5 s/s/y or 1 nucleotide substitution per ORF per 7.5 years; 95% HPD, 1.0–1.8 × 10−5 s/s/y) as compared with TBEV Far-Eastern subtype (3.0 × 10−5 s/s/y or 1 nucleotide substitution per ORF per 3.2 years; 95% HPD, 1.6–4.5 × 10−5 s/s/y). TBEV-common representing the species tick-borne encephalitis virus diverged 9623 years ago (95% HPD interval, 6373–13,208 years). The TBEV Baikalian subtype is the youngest one (489 years; 95% HPD, 291–697 years) which differs significantly by age from TBEV-E (848 years; 95% HPD, 596–1112 years), LIV (2424 years; 95% HPD, 1572–3400 years), TBEV-FE (1936 years, 95% HPD, 1344–2598 years), and the joint clade of TBEV-S (2505 years, 95% HPD, 1700–3421 years) comprising Vasilchenko, Zausaev, and Baltic lineages. [ABSTRACT FROM AUTHOR]

The extreme diversity and complexity of angiosperms is well known. Despite the fact that parasitic plants are angiosperms, little is known about parasitic plant mitogenomic diversity, complexity, and evolution. In this study, we obtained and characterized the mitogenomes of three Cistanche species (holoparasitic plants) from China to compare the repeats, segment duplication and multi-copy protein-coding genes (PCGs), to clarify the phylogenetic and evolution relationship within the Lamiales order, and to identify the mitochondrial plastid insertions (MTPT) in Cistanche mitogenomes. The results showed that the mitogenome sizes of the three Cistanche species ranged from 1,708,661 to 3,978,341 bp. The Cistanche species genome encodes 75–126 genes, including 37–65 PCGs, 31–58 tRNA genes and 3–5 rRNA genes. Compared with other Lamiales and parasitic species, the Cistanche species showed extremely high rates of multi-copy PCGs, ranging from 0.13 to 0.58 percent of the total number of PCGs. In addition, 37–133 Simple Sequence Repeat (SSRs) were found in these three mitogenomes, the majority of which were the mononucleotides Adenine/Thymine. The interspersed repeats contained forward and palindromic repeats. Furthermore, the segment-duplication sequence size ranged from 199,584 to 2,142,551 bp, accounting for 24.9%, 11.7% and 53.9% of the Cistanche deserticola, Cistanche salsa and Cistanche tubulosa mitogenome, respectively. Furthermore, the Ka/Ks analysis suggested that the atp4, ccmB, ccmFc and matR were probably positively selected during Lamiales evolution. The Cistanche plastome suggested the presence of MTPT. Moreover, 6–12 tRNA, 9–15 PCGs fragments and 3 rRNA gene fragments in the Cistanche mitogenomes were found in the MTPT regions. This work reports the Cistanche species mitogenome for the first time, which will be invaluable for study the mitogenome evolution of Orobanchaceae family. [ABSTRACT FROM AUTHOR]

The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subtypes or regions based on 1.8 million high-quality SARS-CoV-2 genomic data. The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) in North America and the United States were always more than 1.0, while the Ka/Ks in other continents and countries showed a sharp decline, then a slow increase to 1.0, and a dramatic increase over time. H1 (B.1) with the highest substitution rate has become the most dominant haplotype subtype since March 2020 and has evolved into multiple haplotype subtypes with smaller substitution rates. Many evolutionary characteristics of early SARS-CoV-2, such as H3 being the only early haplotype subtype that existed for the shortest time, the global prevalence of H1 and H1-5 (B.1.1) within a month after being detected, and many high divergent genome sequences early in February 2020, indicate the missing of early SARS-CoV-2 genomic data. SARS-CoV-2 experienced dynamic selection from December 2019 to August 2021 and has been under strong positive selection since May 2021. Its transmissibility and the ability of immune escape may be greatly enhanced over time. This will bring greater challenges to the control of the pandemic. [ABSTRACT FROM AUTHOR]

Coffee is one of the main traded commodities worldwide, unfortunately, it generates massive amounts of by-products like coffee pulp (CoP), which could be utilized as an alternative feedstuff for cattle contributing to mitigate coffee production environmental damage. The objective of this work was to evaluate the effect of increasing levels of CoP supplementation on milk production, milk composition, and grass dry matter intake (GDMI) by dual-purpose tropical cows. A 4 × 4 Latin square experimental design was conducted, where four multiparous dual-purpose Holstein x Cebu cows with an average live weight of 477 ± 7 kg and milk yield of 12.1 ± 2.7 kg/d were used. The cows grazed 10 h/d on a Cynodon plectostachius sward with a stocking rate of three cows/ha. All cows received 6 kg/d DM of an experimental concentrate (EC), and the treatments consisted of four supplementation levels of CoP: T1 = 0, T2 = 0.6, T3 = 0.9, and T4 = 1.2 kg DM/d, which was provided on top of the concentrate and mixed with the EC. Grass intake was determined by the n-alkanes technique. A significant difference was observed for the average total daily DM intake (p < 0.02). No significant differences (p > 0.05) were observed for milk yield, milk composition, body weight, and GDMI for all the inclusion levels of CoP. It was concluded that CoP can be included at levels of 0.6 to 0.9 kg DM/d in the diets of cows without compromising milk yield or GDMI. [ABSTRACT FROM AUTHOR]

The degree of antigenic drift in swine influenza A viruses (swIAV) has historically been regarded as minimal compared to that of human influenza A virus strains. However, as surveillance activities on swIAV have increased, more isolates have been characterized, revealing a high level of genetic and antigenic differences even within the same swIAV lineage. The objective of this study was to investigate the level of genetic drift in one enzootically infected swine herd over one year. Nasal swabs were collected monthly from sows (n = 4) and piglets (n = 40) in the farrowing unit, and from weaners (n = 20) in the nursery. Virus from 1–4 animals were sequenced per month. Analyses of the sequences revealed that the hemagglutinin (HA) gene was the main target for genetic drift with a substitution rate of 7.6 × 10−3 substitutions/site/year and evidence of positive selection. The majority of the mutations occurred in the globular head of the HA protein and in antigenic sites. The phylogenetic tree of the HA sequences displayed a pectinate typology, where only a single lineage persists and forms the ancestor for subsequent lineages. This was most likely caused by repeated selection of a single immune-escape variant, which subsequently became the founder of the next wave of infections. [ABSTRACT FROM AUTHOR]

Seoul virus (SEOV), which causes hemorrhagic fever with renal syndrome (HFRS) in humans, has spread all over the world, especially in mainland China. Understanding basic mechanisms of SEOV evolution is essential to better combat and prevent viral diseases. Here, we examined SEOV prevalence and evolution in the residential area of four districts in Guangzhou city, China. The carriage of SEOV was observed in 33.33% of the sampled rodents, with 35.96% of the sampled Rattus norvegicus and 13.33% of R. tanezumi. Based on the comprehensive analyses of large (L), medium (M), and small (S) segments, our study first demonstrated that the genetic characterization of urban SEOV was shaped by high nucleotide substitution rates, purifying selection, and recombination. Additionally, we detected mutational saturation in the S segment of SEOV, which may lead to the biases of genetic divergence and substitution rates in our study. Importantly, we have filled the gap of SEOV evolution in the urban area. The genetic variation of SEOV may highlight the risk of HFRS, which merits further investigation. [ABSTRACT FROM AUTHOR]

The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, the chloroplast (cp) genomes of 13 taxa within the Myrsinaceae s.str. clade are sequenced and characterized. These cp genomes are typical quadripartite circle molecules and are highly conserved in size and gene content. Three pseudogenes are identified, of which ycf15 is totally absent from five taxa. Noncoding and large single copy region (LSC) exhibit higher levels of nucleotide diversity (Pi) than other regions. A total of ten hotspot fragments and 796 chloroplast simple sequence repeats (SSR) loci are found across all cp genomes. The results of phylogenetic analysis support the notion that the monophyletic Myrsinaceae s.str. clade has two subclades. Non-synonymous substitution rates (dN) are higher in housekeeping (HK) genes than photosynthetic (PS) genes, but both groups have a nearly identical synonymous substitution rate (dS). The results indicate that the PS genes are under stronger functional constraints compared with the HK genes. Overall, the study provides hypervariable molecular markers for phylogenetic reconstruction and contributes to a better understanding of plastid gene evolution in Myrsinaceae s.str. clade. [ABSTRACT FROM AUTHOR]

Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of Synechococcus-infecting Myoviridae ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10−5 substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity. [ABSTRACT FROM AUTHOR]

A throttle can be installed on the intake pipe of a natural gas (NG)/diesel dual-fuel engine to control the excess air ratio of the air-fuel mixture by adjusting the air intake. Building on a previously proposed NG/diesel dual-fuel supply strategy using the adjustment of excess air ratio, this work further studied the effects of different injection timing schemes on output power, fuel efficiency, and pollutant emissions of a dual-fuel engine under low to medium load conditions. In the experiment, the engine was operated at a speed of 1600 r/min, under either low (27.1 N·m) or medium (50.6 N·m) loads, and the NG substitution rate was either 40%, 60%, or 80%. The effect of different injection timing schemes on the combustion performance of the engine under low to medium load conditions was studied based on in-cylinder pressure changes detected by a pressure sensor. Experimental results showed that under medium-speed low-load conditions and a NG substitution rate of 40%, setting the diesel injection timing to 27 °CA BTDC increased the engine output power by 9.03%, reduced the brake specific energy consumption (BSEC) by 13.33%, and effectively reduced CO, CO2, and HC emissions. Under medium-speed medium-load conditions with a NG substitution rate of 80%, setting the diesel injection timing to 25 °CA BTDC increased the engine output power by 14.62%, reduced the BSEC by 11.73%, and significantly reduced CO, CO2, and HC emissions. [ABSTRACT FROM AUTHOR]

Lowering the amount of excess air is believed to increase the density of the air-fuel mixture and help improve the combustion rate for compression ignition engines. This paper proposes an approach of adding a throttle body at the intake pipe to control the excess air ratio with reduction of air supply to achieve a better balance between the power, emissions and fuel efficiency at medium and low load of a natural gas dual-fuel diesel engine converted from a conventional diesel engine. Various experiments in both pure diesel and dual-fuel mode under intermediate engine speed are performed with the proposed critical method of excess air ratio control. The experimental results reveal that better excess air ratio is very beneficial for the power output and brake specific energy consumption in dual-fuel combustion under medium and low load conditions. Moreover, the substitution rate can reach as high as 40% under low load conditions with throttle control. [ABSTRACT FROM AUTHOR]